4ynk - Revision history

OCA at 15:37, 8 November 2023

OCA — Wed, 08 Nov 2023 15:37:23 GMT

←Older revision		Revision as of 15:37, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ynk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YNK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ynk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YNK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YW2:(1R,3R,7E,17BETA)-17-{(5S)-5-HYDROXY-5-[(3R,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]PENTA-1,3-DIYN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YW2</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YW2:(1R,3R,7E,17BETA)-17-{(5S)-5-HYDROXY-5-[(3R,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]PENTA-1,3-DIYN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YW2</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ynk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ynk OCA], [https://pdbe.org/4ynk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ynk RCSB], [https://www.ebi.ac.uk/pdbsum/4ynk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ynk ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ynk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ynk OCA], [https://pdbe.org/4ynk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ynk RCSB], [https://www.ebi.ac.uk/pdbsum/4ynk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ynk ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:21, 3 May 2023

OCA — Wed, 03 May 2023 08:21:24 GMT

←Older revision		Revision as of 08:21, 3 May 2023
Line 3:		Line 3:
	<StructureSection load='4ynk' size='340' side='right'caption='[[4ynk]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4ynk' size='340' side='right'caption='[[4ynk]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ynk]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YNK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YNK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ynk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YNK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YW2:(1R,3R,7E,17BETA)-17-{(5S)-5-HYDROXY-5-[(3R,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]PENTA-1,3-DIYN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YW2</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=YW2:(1R,3R,7E,17BETA)-17-{(5S)-5-HYDROXY-5-[(3R,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]PENTA-1,3-DIYN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YW2</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])~~</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ynk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ynk OCA], [https://pdbe.org/4ynk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ynk RCSB], [https://www.ebi.ac.uk/pdbsum/4ynk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ynk ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ynk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ynk OCA], [~~http~~://pdbe.org/4ynk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ynk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ynk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ynk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VDR_RAT VDR_RAT]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref>	+	[https://www.uniprot.org/uniprot/VDR_RAT VDR_RAT] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:

	==See Also==		==See Also==
-	*[[Vitamin D receptor\|Vitamin D receptor]]	+	*[[Vitamin D receptor 3D structures\|Vitamin D receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Buffalo rat~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ikura, T~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Ito, N~~]]	+	[[Category: Ikura T]]
-	[[Category: ~~Watarai, Y~~]]	+	[[Category: Ito N]]
-	[[Category: ~~Hormone receptor]]~~	+	[[Category: Watarai Y]]
-	~~[[Category: Transcription~~]]	+

OCA at 06:48, 12 June 2019

OCA — Wed, 12 Jun 2019 06:48:58 GMT

←Older revision		Revision as of 06:48, 12 June 2019
Line 1:		Line 1:
		+
	==Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound==		==Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound==
-	<StructureSection load='4ynk' size='340' side='right' caption='[[4ynk]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4ynk' size='340' side='right'caption='[[4ynk]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ynk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YNK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ynk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YNK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YW2:(1R,3R,7E,17BETA)-17-{(5S)-5-HYDROXY-5-[(3R,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]PENTA-1,3-DIYN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YW2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YW2:(1R,3R,7E,17BETA)-17-{(5S)-5-HYDROXY-5-[(3R,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]PENTA-1,3-DIYN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YW2</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ynk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ynk OCA], [http://pdbe.org/4ynk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ynk RCSB], [http://www.ebi.ac.uk/pdbsum/4ynk PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Vdr, Nr1i1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ynk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ynk OCA], [http://pdbe.org/4ynk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ynk RCSB], [http://www.ebi.ac.uk/pdbsum/4ynk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ynk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4ynk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ynk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Vitamin D receptor\|Vitamin D receptor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Ikura, T]]		[[Category: Ikura, T]]
	[[Category: Ito, N]]		[[Category: Ito, N]]

OCA at 16:59, 20 January 2016

OCA — Wed, 20 Jan 2016 16:59:32 GMT

←Older revision		Revision as of 16:59, 20 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound==
		+	<StructureSection load='4ynk' size='340' side='right' caption='[[4ynk]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ynk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YNK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=YW2:(1R,3R,7E,17BETA)-17-{(5S)-5-HYDROXY-5-[(3R,5R,7R)-TRICYCLO[3.3.1.1~3,7~]DEC-1-YL]PENTA-1,3-DIYN-1-YL}-2-METHYLIDENE-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL'>YW2</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ynk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ynk OCA], [http://pdbe.org/4ynk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ynk RCSB], [http://www.ebi.ac.uk/pdbsum/4ynk PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VDR_RAT VDR_RAT]] Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.<ref>PMID:17227670</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Novel 19-norvitamin D analogues (ADYW1-4, 5a-d) in which an adamantyl diyne side chain is attached directly to the 17-position of the D ring are designed and stereoselectively synthesized. The adamantane ring of these analogues was expected to interfere with helix 12 (H12, activation function 2) of the vitamin D receptor (VDR) to modulate its activities. The analogue 5b binds to the VDR (7% of the natural hormone) and shows significant partial agonistic activity in transactivation assay. Compound 5b showed considerable selectivity in VDR target genes expressions in vitro, it was taken up by target cells 2-3 times more readily, and its lifetime was three times longer than the natural hormone. The X-ray crystal structure of 5b in complex with VDR reveals that the ligand binds similarly to the natural hormone, but the diyne moiety is slightly bent (angles around the diyne 5 degrees to 8 degrees ) with respect to the original diyne vitamin D compound 6 in VDR (<1 degrees ) due to steric hindrance with helix 12.

-	~~The entry 4ynk is ON HOLD until Paper Publication~~	+	Synthesis, Biological Activities, and X-ray Crystal Structural Analysis of 25-Hydroxy-25(or 26)-adamantyl-17-[20(22),23-diynyl]-21-norvitamin D Compounds.,Watarai Y, Ishizawa M, Ikura T, Zacconi FC, Uno S, Ito N, Mourino A, Tokiwa H, Makishima M, Yamada S J Med Chem. 2015 Dec 24;58(24):9510-21. doi: 10.1021/acs.jmedchem.5b00792. Epub, 2015 Dec 15. PMID:26613420<ref>PMID:26613420</ref>

-	~~Authors: Watarai~~, Y.~~, Ikura, T~~.~~, Ito, N~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of vitamin D receptor ligand binding domain complexed with a 19~~-~~norvitamin D compound~~	+	<div class="pdbe-citations 4ynk" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ikura, T]]
	[[Category: Ito, N]]		[[Category: Ito, N]]
	[[Category: Watarai, Y]]		[[Category: Watarai, Y]]
-	[[Category: ~~Ikura, T~~]]	+	[[Category: Hormone receptor]]
		+	[[Category: Transcription]]

OCA at 10:03, 13 May 2015

OCA — Wed, 13 May 2015 10:03:00 GMT

←Older revision		Revision as of 10:03, 13 May 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ynk is ON HOLD	+	The entry 4ynk is ON HOLD until Paper Publication

	Authors: Watarai, Y., Ikura, T., Ito, N.		Authors: Watarai, Y., Ikura, T., Ito, N.

OCA: Protected "4ynk" [edit=sysop:move=sysop]

OCA — Wed, 18 Mar 2015 10:54:40 GMT

Protected "4ynk" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:54, 18 March 2015

OCA: New page: '''Unreleased structure''' The entry 4ynk is ON HOLD Authors: Watarai, Y., Ikura, T., Ito, N. Description: Crystal structure of vitamin D receptor ligand binding domain complexed with ...

OCA — Wed, 18 Mar 2015 10:54:39 GMT

New page: '''Unreleased structure''' The entry 4ynk is ON HOLD Authors: Watarai, Y., Ikura, T., Ito, N. Description: Crystal structure of vitamin D receptor ligand binding domain complexed with ...

New page

'''Unreleased structure'''

The entry 4ynk is ON HOLD

Authors: Watarai, Y., Ikura, T., Ito, N.

Description: Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound
[[Category: Unreleased Structures]]
[[Category: Ito, N]]
[[Category: Watarai, Y]]
[[Category: Ikura, T]]